6juo - Revision history

OCA at 10:20, 22 November 2023

OCA — Wed, 22 Nov 2023 10:20:06 GMT

←Older revision		Revision as of 10:20, 22 November 2023
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	<StructureSection load='6juo' size='340' side='right'caption='[[6juo]], [[Resolution\|resolution]] 2.16Å' scene=''>		<StructureSection load='6juo' size='340' side='right'caption='[[6juo]], [[Resolution\|resolution]] 2.16Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[6juo]] is a 6 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6JUO OCA]. For a <b>guided tour on the structure components</b> use [~~http~~://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=6JUO FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[6juo]] is a 6 chain structure with sequence from [https://en.wikipedia.org/wiki/Mycolicibacterium_smegmatis Mycolicibacterium smegmatis] and [https://en.wikipedia.org/wiki/Mycolicibacterium_smegmatis_MC2_155 Mycolicibacterium smegmatis MC2 155]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6JUO OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=6JUO FirstGlance]. <br>
-	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=0KX:2-DEOXY-5-O-[(R)-HYDROXY{[(R)-HYDROXY(PHOSPHONOOXY)PHOSPHORYL]AMINO}PHOSPHORYL]CYTIDINE'>0KX</scene>, <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene~~></td></tr>~~	+	</td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models\|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution\|Resolution]] 2.16Å</td></tr>
-	<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/DNA-directed_DNA_polymerase DNA-directed DNA polymerase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=2.7.7.7 2.7.7.7] </span></td></tr>	+	<tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=0KX:2-DEOXY-5-O-[(R)-HYDROXY{[(R)-HYDROXY(PHOSPHONOOXY)PHOSPHORYL]AMINO}PHOSPHORYL]CYTIDINE'>0KX</scene>, <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene></td></tr>
-	<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[~~http~~://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=6juo FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6juo OCA], [~~http~~://pdbe.org/6juo PDBe], [~~http~~://www.rcsb.org/pdb/explore.do?structureId=6juo RCSB], [~~http~~://www.ebi.ac.uk/pdbsum/6juo PDBsum], [~~http~~://prosat.h-its.org/prosat/prosatexe?pdbcode=6juo ProSAT]</span></td></tr>	+	<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=6juo FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6juo OCA], [https://pdbe.org/6juo PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=6juo RCSB], [https://www.ebi.ac.uk/pdbsum/6juo PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=6juo ProSAT]</span></td></tr>
	</table>		</table>
	== Function ==		== Function ==
-	[~~[http~~://www.uniprot.org/uniprot/A0QR77_MYCS2 A0QR77_MYCS2]] Poorly processive, error-prone DNA polymerase involved in untargeted mutagenesis. Copies undamaged DNA at stalled replication forks, which arise in vivo from mismatched or misaligned primer ends. These misaligned primers can be extended by PolIV. Exhibits no 3'-5' exonuclease (proofreading) activity. May be involved in translesional synthesis, in conjunction with the beta clamp from PolIII (By similarity).[HAMAP-Rule:MF_01113]	+	[https://www.uniprot.org/uniprot/A0QR77_MYCS2 A0QR77_MYCS2] Poorly processive, error-prone DNA polymerase involved in untargeted mutagenesis. Copies undamaged DNA at stalled replication forks, which arise in vivo from mismatched or misaligned primer ends. These misaligned primers can be extended by PolIV. Exhibits no 3'-5' exonuclease (proofreading) activity. May be involved in translesional synthesis, in conjunction with the beta clamp from PolIII (By similarity).[HAMAP-Rule:MF_01113]
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">
	== Publication Abstract from PubMed ==		== Publication Abstract from PubMed ==
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	</div>		</div>
	<div class="pdbe-citations 6juo" style="background-color:#fffaf0;"></div>		<div class="pdbe-citations 6juo" style="background-color:#fffaf0;"></div>
		+
		+	==See Also==
		+	*[[DNA polymerase 3D structures\|DNA polymerase 3D structures]]
	== References ==		== References ==
	<references/>		<references/>
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
-	[[Category: DNA-directed DNA polymerase]]
	[[Category: Large Structures]]		[[Category: Large Structures]]
-	[[Category: ~~Johnson, M K~~]]	+	[[Category: Mycolicibacterium smegmatis]]
-	[[Category: ~~Nair, D T~~]]	+	[[Category: Mycolicibacterium smegmatis MC2 155]]
-	[[Category: ~~Dna polymerase~~]]	+	[[Category: Johnson MK]]
-	[[Category: ~~Replication]]~~	+	[[Category: Nair DT]]
-	~~[[Category: Replication-dna complex~~]]	+

OCA at 06:18, 19 February 2020

OCA — Wed, 19 Feb 2020 06:18:49 GMT

←Older revision		Revision as of 06:18, 19 February 2020
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-	'''Unreleased structure'''

-	~~The entry~~ 6juo is ~~ON HOLD until Paper~~ Publication	+	==MsDpo4-DNA complex 4==
		+	<StructureSection load='6juo' size='340' side='right'caption='[[6juo]], [[Resolution\|resolution]] 2.16Å' scene=''>
		+	== Structural highlights ==
		+	<table><tr><td colspan='2'>[[6juo]] is a 6 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6JUO OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=6JUO FirstGlance]. <br>
		+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=0KX:2-DEOXY-5-O-[(R)-HYDROXY{[(R)-HYDROXY(PHOSPHONOOXY)PHOSPHORYL]AMINO}PHOSPHORYL]CYTIDINE'>0KX</scene>, <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene></td></tr>
		+	<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/DNA-directed_DNA_polymerase DNA-directed DNA polymerase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=2.7.7.7 2.7.7.7] </span></td></tr>
		+	<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=6juo FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6juo OCA], [http://pdbe.org/6juo PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=6juo RCSB], [http://www.ebi.ac.uk/pdbsum/6juo PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=6juo ProSAT]</span></td></tr>
		+	</table>
		+	== Function ==
		+	[[http://www.uniprot.org/uniprot/A0QR77_MYCS2 A0QR77_MYCS2]] Poorly processive, error-prone DNA polymerase involved in untargeted mutagenesis. Copies undamaged DNA at stalled replication forks, which arise in vivo from mismatched or misaligned primer ends. These misaligned primers can be extended by PolIV. Exhibits no 3'-5' exonuclease (proofreading) activity. May be involved in translesional synthesis, in conjunction with the beta clamp from PolIII (By similarity).[HAMAP-Rule:MF_01113]
		+	<div style="background-color:#fffaf0;">
		+	== Publication Abstract from PubMed ==
		+	The presence of ribonucleotides in DNA can lead to genomic instability and cellular lethality. To prevent adventitious rNTP incorporation, the majority of the DNA polymerases (dPols) possess a steric filter. The dPol named MsDpo4 (Mycobacterium smegmatis) naturally lacks this steric filter and hence is capable of rNTP addition. The introduction of the steric filter in MsDpo4 did not result in complete abrogation of the ability of this enzyme to incorporate ribonucleotides. In comparison, DNA polymerase IV (PolIV) from Escherichia coli exhibited stringent selection for deoxyribonucleotides. A comparison of MsDpo4 and PolIV led to the discovery of an additional polar filter responsible for sugar selectivity. Thr43 represents the filter in PolIV and this residue forms interactions with the incoming nucleotide to draw it closer to the enzyme surface. As a result, the 2'-OH in rNTPs will clash with the enzyme surface, and therefore ribonucleotides cannot be accommodated in the active site in a conformation compatible with productive catalysis. The substitution of the equivalent residue in MsDpo4-Cys47, with Thr led to a drastic reduction in the ability of the mycobacterial enzyme to incorporate rNTPs. Overall, our studies evince that the polar filter serves to prevent ribonucleotide incorporation by dPols.

-	~~Authors~~:	+	A polar filter in DNA polymerases prevents ribonucleotide incorporation.,Johnson MK, Kottur J, Nair DT Nucleic Acids Res. 2019 Nov 18;47(20):10693-10705. doi: 10.1093/nar/gkz792. PMID:31544946<ref>PMID:31544946</ref>

-	~~Description~~:	+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
-	[[Category: ~~Unreleased~~ Structures]]	+	</div>
		+	<div class="pdbe-citations 6juo" style="background-color:#fffaf0;"></div>
		+	== References ==
		+	<references/>
		+	__TOC__
		+	</StructureSection>
		+	[[Category: DNA-directed DNA polymerase]]
		+	[[Category: Large Structures]]
		+	[[Category: Johnson, M K]]
		+	[[Category: Nair, D T]]
		+	[[Category: Dna polymerase]]
		+	[[Category: Replication]]
		+	[[Category: Replication-dna complex]]

OCA at 04:02, 19 June 2019

OCA — Wed, 19 Jun 2019 04:02:14 GMT

←Older revision		Revision as of 04:02, 19 June 2019
Line 1:		Line 1:
	'''Unreleased structure'''		'''Unreleased structure'''

-	The entry 6juo is ON HOLD	+	The entry 6juo is ON HOLD until Paper Publication

	Authors:		Authors:

OCA: Protected "6juo" [edit=sysop:move=sysop]

OCA — Wed, 24 Apr 2019 04:45:37 GMT

Protected "6juo" [edit=sysop:move=sysop]

←Older revision

Revision as of 04:45, 24 April 2019

OCA: New page: '''Unreleased structure''' The entry 6juo is ON HOLD Authors: Description: Category: Unreleased Structures

OCA — Wed, 24 Apr 2019 04:45:36 GMT

New page: '''Unreleased structure''' The entry 6juo is ON HOLD Authors: Description: Category: Unreleased Structures

New page

'''Unreleased structure'''

The entry 6juo is ON HOLD

Authors:

Description:
[[Category: Unreleased Structures]]